General information for g79.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Paired box protein Pax-6.
Parent gene
- The parent gene g79 is located on chr_3: 733020..742441 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g79 | g79.t1 | TSS | g79.t1 | 732562 | 732562 |
| chr_3 | g79 | g79.t1 | isoform | g79.t1 | 733020 | 742441 |
| chr_3 | g79 | g79.t1 | exon | g79.t1.exon1 | 733020 | 733094 |
| chr_3 | g79 | g79.t1 | cds | g79.t1.CDS1 | 733020 | 733094 |
| chr_3 | g79 | g79.t1 | exon | g79.t1.exon2 | 733155 | 733176 |
| chr_3 | g79 | g79.t1 | cds | g79.t1.CDS2 | 733155 | 733176 |
| chr_3 | g79 | g79.t1 | exon | g79.t1.exon3 | 733705 | 733828 |
| chr_3 | g79 | g79.t1 | cds | g79.t1.CDS3 | 733705 | 733828 |
| chr_3 | g79 | g79.t1 | exon | g79.t1.exon4 | 733892 | 734072 |
| chr_3 | g79 | g79.t1 | cds | g79.t1.CDS4 | 733892 | 734072 |
| chr_3 | g79 | g79.t1 | exon | g79.t1.exon5 | 737597 | 737822 |
| chr_3 | g79 | g79.t1 | cds | g79.t1.CDS5 | 737597 | 737822 |
| chr_3 | g79 | g79.t1 | exon | g79.t1.exon6 | 742007 | 742180 |
| chr_3 | g79 | g79.t1 | cds | g79.t1.CDS6 | 742007 | 742180 |
| chr_3 | g79 | g79.t1 | exon | g79.t1.exon7 | 742302 | 742441 |
| chr_3 | g79 | g79.t1 | cds | g79.t1.CDS7 | 742302 | 742441 |
| chr_3 | g79 | g79.t1 | TTS | g79.t1 | NA | NA |
Sequences
>g79.t1 Gene=g79 Length=942
ATGCATCAACATGCAACGATTGGTCAAACATCGCTCTTTGGCTGCTCATCGGCTGGCCAT
AGTGGCATTAATCAGCTAGGAGGCGTTTATGTCAATGGTCGACCACTGCCAGATTCAACT
AGACAAAAGATTGTAGAATTGGCCCATTCAGGAGCGCGACCTTGTGATATTTCTCGCATA
TTACAGGTCTCAAATGGATGTGTTAGTAAAATATTAGGAAGATATTATGAAACTGGCTCA
ATAAAGCCTAGAGCGATAGGTGGATCAAAACCACGTGTAGCAACAGCAAATGTCGTCAAT
AAAATTGCTGATTATAAAAGAGAATGTCCATCAATTTTTGCATGGGAAATTCGTGATCGG
TTGCTATCAGATGGTGTATGCAATAGTGACAATATTCCAAGTGTTTCATCAATAAATCGG
GTATTAAGGAATTTAGCATCGCAAAAGGAACAACAGTCAACACAAAATGATTCCGTCTAT
GATAAATTGAGAATGTTCAATGGTCAGTCAGGTGGATGGGCTTGGTATCCAACGAGTAAT
GCTGCACCAACACATCTTTCACTACCTCCAACACCAACATCAGCACAGCTTAGCGGGCAA
TTGACTCGTGAAGAATTACAAAAACGTGATCTCTTTTCGGTAGATATTCAACAATCAAGT
TTACATGAGAGCACATCAGATGGAAATTCTGAACATAATTCATCAGGTGATGAAGATTCA
CAAATGCGTTTACGACTTAAAAGAAAATTACAACGAAATCGTACATCTTTTACAAATGAA
CAAATTGATAGTCTTGAAAAAGAATTCGAGAGAACGCACTATCCTGATGTATTTGCAAGA
GAACGATTAGCCGAGAAAATAGGATTACCCGAGGCAAGAATACAGGTACTTTTACAGCAA
CACGAAAAGTCGGTAAACATAAAATGCCAATTAAAACGATAA
>g79.t1 Gene=g79 Length=313
MHQHATIGQTSLFGCSSAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRI
LQVSNGCVSKILGRYYETGSIKPRAIGGSKPRVATANVVNKIADYKRECPSIFAWEIRDR
LLSDGVCNSDNIPSVSSINRVLRNLASQKEQQSTQNDSVYDKLRMFNGQSGGWAWYPTSN
AAPTHLSLPPTPTSAQLSGQLTREELQKRDLFSVDIQQSSLHESTSDGNSEHNSSGDEDS
QMRLRLKRKLQRNRTSFTNEQIDSLEKEFERTHYPDVFARERLAEKIGLPEARIQVLLQQ
HEKSVNIKCQLKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g79.t1 | CDD | cd00131 | PAX | 19 | 146 | 6.15778E-83 |
| 15 | g79.t1 | CDD | cd00086 | homeodomain | 252 | 296 | 1.38797E-13 |
| 13 | g79.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 13 | 87 | 9.9E-42 |
| 12 | g79.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 88 | 165 | 1.3E-33 |
| 11 | g79.t1 | Gene3D | G3DSA:1.10.10.60 | - | 243 | 307 | 3.8E-18 |
| 19 | g79.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 218 | 242 | - |
| 3 | g79.t1 | PANTHER | PTHR45636 | PAIRED BOX PROTEIN PAX-6-RELATED-RELATED | 6 | 305 | 1.9E-171 |
| 4 | g79.t1 | PANTHER | PTHR45636:SF29 | GH14454P | 6 | 305 | 1.9E-171 |
| 8 | g79.t1 | PRINTS | PR00027 | Paired box signature | 23 | 38 | 5.1E-42 |
| 7 | g79.t1 | PRINTS | PR00027 | Paired box signature | 41 | 59 | 5.1E-42 |
| 6 | g79.t1 | PRINTS | PR00027 | Paired box signature | 61 | 78 | 5.1E-42 |
| 5 | g79.t1 | PRINTS | PR00027 | Paired box signature | 79 | 96 | 5.1E-42 |
| 2 | g79.t1 | Pfam | PF00292 | ‘Paired box’ domain | 19 | 143 | 2.4E-70 |
| 1 | g79.t1 | Pfam | PF00046 | Homeodomain | 252 | 296 | 2.4E-13 |
| 18 | g79.t1 | ProSitePatterns | PS00034 | Paired DNA-binding domain signature. | 53 | 69 | - |
| 21 | g79.t1 | ProSiteProfiles | PS51057 | Paired DNA-binding domain profile. | 19 | 145 | 62.852 |
| 20 | g79.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 248 | 308 | 12.357 |
| 16 | g79.t1 | SMART | SM00351 | pax3 | 19 | 143 | 5.8E-90 |
| 17 | g79.t1 | SMART | SM00389 | HOX_1 | 250 | 312 | 1.1E-11 |
| 10 | g79.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 21 | 144 | 2.99E-38 |
| 9 | g79.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 234 | 296 | 4.6E-14 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003677 | DNA binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K08031 (paired box protein 6)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed